Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-ballot built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

: Knowledge Base Codes - XML Representation

Page standards status: Informative

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<CodeSystem xmlns="http://hl7.org/fhir">
  <id value="knowledge-base-cs"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: CodeSystem knowledge-base-cs</b></p><a name="knowledge-base-cs"> </a><a name="hcknowledge-base-cs"> </a><p>This case-insensitive code system <code>http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/knowledge-base-cs</code> defines the following codes:</p><table class="codes"><tr><td style="white-space:nowrap"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td style="white-space:nowrap">gnomadv4.1exome<a name="knowledge-base-cs-gnomadv4.461exome"> </a></td><td>gnomad v4.1 exome</td><td>gnomAD version 4.1 exome</td></tr><tr><td style="white-space:nowrap">gnomadv4.1genome<a name="knowledge-base-cs-gnomadv4.461genome"> </a></td><td>gnomad v4.1 genome</td><td>gnomAD version 4.1 genome</td></tr><tr><td style="white-space:nowrap">clinvar-april2024<a name="knowledge-base-cs-clinvar-april2024"> </a></td><td>clinvar april 2024</td><td>Clinvar April 2024 release</td></tr><tr><td style="white-space:nowrap">clinvar-march2024<a name="knowledge-base-cs-clinvar-march2024"> </a></td><td>clinvar march 2024</td><td>Clinvar March 2024 release</td></tr><tr><td style="white-space:nowrap">1000genomesv4.1.0<a name="knowledge-base-cs-1000genomesv4.461.460"> </a></td><td>1000genomes v4.1.0</td><td>1000genomes version 4.1.0</td></tr><tr><td style="white-space:nowrap">civicv1.2.0<a name="knowledge-base-cs-civicv1.462.460"> </a></td><td>civic v1.2.0</td><td>CIViC version 1.2.0</td></tr><tr><td style="white-space:nowrap">graspv2.1.0<a name="knowledge-base-cs-graspv2.461.460"> </a></td><td>grasp v2.1.0</td><td>GRASP version 2.1.0</td></tr><tr><td style="white-space:nowrap">oncokbv1.5.2<a name="knowledge-base-cs-oncokbv1.465.462"> </a></td><td>oncokb v1.5.2</td><td>OncoKB version 1.5.2</td></tr><tr><td style="white-space:nowrap">pharmgkbv2.3.5<a name="knowledge-base-cs-pharmgkbv2.463.465"> </a></td><td>pharmgkb v2.3.5</td><td>PharmGKB version 2.3.5</td></tr><tr><td style="white-space:nowrap">phastconsv3.6.0<a name="knowledge-base-cs-phastconsv3.466.460"> </a></td><td>phascons v.3.6.0</td><td>PhastCons version 3.6.0</td></tr></table></div>
  </text>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
    <valueCode value="cg"/>
  </extension>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
    <valueCode value="informative">
      <extension
                 url="http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom">
        <valueCanonical
                        value="http://hl7.org/fhir/uv/genomics-reporting/ImplementationGuide/genomics-reporting"/>
      </extension>
    </valueCode>
  </extension>
  <url
       value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/knowledge-base-cs"/>
  <version value="4.0.0-ballot"/>
  <name value="KnowledgeBaseCS"/>
  <title value="Knowledge Base Codes"/>
  <status value="active"/>
  <experimental value="true"/>
  <date value="2025-06-24T17:31:37+00:00"/>
  <publisher value="HL7 International / Clinical Genomics"/>
  <contact>
    <name value="HL7 International / Clinical Genomics"/>
    <telecom>
      <system value="url"/>
      <value value="http://www.hl7.org/Special/committees/clingenomics"/>
    </telecom>
    <telecom>
      <system value="email"/>
      <value value="cg@lists.HL7.org"/>
    </telecom>
  </contact>
  <description
               value="This example code systems provides examples on how to properly display the knowledge base version number. Version numbers should always be followed by the letter v and calendar dates are displayed Month Day Year. For clarity the month SHALL be written in full."/>
  <jurisdiction>
    <coding>
      <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
      <code value="001"/>
      <display value="World"/>
    </coding>
  </jurisdiction>
  <caseSensitive value="false"/>
  <content value="complete"/>
  <count value="10"/>
  <concept>
    <code value="gnomadv4.1exome"/>
    <display value="gnomad v4.1 exome"/>
    <definition value="gnomAD version 4.1 exome"/>
  </concept>
  <concept>
    <code value="gnomadv4.1genome"/>
    <display value="gnomad v4.1 genome"/>
    <definition value="gnomAD version 4.1 genome"/>
  </concept>
  <concept>
    <code value="clinvar-april2024"/>
    <display value="clinvar april 2024"/>
    <definition value="Clinvar April 2024 release"/>
  </concept>
  <concept>
    <code value="clinvar-march2024"/>
    <display value="clinvar march 2024"/>
    <definition value="Clinvar March 2024 release"/>
  </concept>
  <concept>
    <code value="1000genomesv4.1.0"/>
    <display value="1000genomes v4.1.0"/>
    <definition value="1000genomes version 4.1.0"/>
  </concept>
  <concept>
    <code value="civicv1.2.0"/>
    <display value="civic v1.2.0"/>
    <definition value="CIViC version 1.2.0"/>
  </concept>
  <concept>
    <code value="graspv2.1.0"/>
    <display value="grasp v2.1.0"/>
    <definition value="GRASP version 2.1.0"/>
  </concept>
  <concept>
    <code value="oncokbv1.5.2"/>
    <display value="oncokb v1.5.2"/>
    <definition value="OncoKB version 1.5.2"/>
  </concept>
  <concept>
    <code value="pharmgkbv2.3.5"/>
    <display value="pharmgkb v2.3.5"/>
    <definition value="PharmGKB version 2.3.5"/>
  </concept>
  <concept>
    <code value="phastconsv3.6.0"/>
    <display value="phascons v.3.6.0"/>
    <definition value="PhastCons version 3.6.0"/>
  </concept>
</CodeSystem>